During installation process select the folder with original game's files ('E:\Games\Quake II' in my case) as an installation path.

Complete the installation and start the game by running 'egl.exe' from the game's directory.

Open 'Video'->'Video Settings'. Select an appropriate 'Resolution'. Set 'Trilinear' for 'Texture Mode', '32 Bit' for 'Bit Depth', turn on 'Stencil Buffer' and set 'Texture Quality' to maximum.

Open 'Video'->'OpenGL Extensions'. Ensure that everything is set to 'Yes' excluding the 'Texture Compression'. Set 'Maximum Anisotropy' to a maximum value.

Open 'Options'->'Controls' to adjust your in-game controls.

Open 'Options'->'Effects'. Set 'Smoke Lingering' to '10', turn on 'Particle Culling' and 'Particle Ligthning'. Turn on 'Explosion Rattling' and set 'Rattle Severity' to maximum.Ensure that 'Decals' and 'Decal LOD' are turned on and 'Decal Life', 'Burn Life' and 'Max Decals' are set to maximum.Ensure that 'Caustics' and 'Detail Textures' are turned on.

Turn on 'Always Run' and 'Mouse look' in 'Options'->'Input'.

Open 'Options'->'Misc'. Set 'Alias Shadows' to 'Stencil'.

Open 'Options'->'Sound'. Set 'Sound Quality' to a maximum supported by your hardware.